The Sha’ar Hakavanot (collection of Kabbalistic teachings) writes that after one counts the Omer – meaning, after reciting the Beracha and then counting that day’s number – one should offer a prayer for the rebuilding of the Bet Hamikdash. The text of this prayer is, "Harahaman Hu Yahazir Abodat Bet Hamikdash Limkomah Bimhera Beyamenu Amen" ("The Merciful One shall restore the service of the Temple to its place, speedily and in our days, Amen").
The reason for this practice is that according to most Halachic authorities, the Misva of counting the Omer applies nowadays Mi’de’rabbanan – by force of Rabbinic enactment – as opposed to Torah law. The Torah obligation of Sefirat Ha’omer applied only in the times of the Bet Hamikdash, when we offered the special Omer sacrifice, whereas nowadays, in the absence of Bet Hamikdash, when we cannot bring this offering, our counting is only commemorative. Therefore, after we count the Omer each night, we pray to God to rebuild the Bet Hamikdash so we can offer the Korban Ha’omer, and then we will be able to count in fulfillment of the actual Misva. And even according to those authorities (such as the Rambam) who maintained that Sefirat Ha’omer is required by Torah law nowadays, we offer a prayer that the Temple will be rebuilt so we can offer the Korban Ha’omer.
This also answers the question addressed by the Halachic authorities as to why we do not recite the Beracha of "Shehehiyanu" the first time we count the Omer each year. As we know, whenever we perform a Misva that presents itself on infrequent occasions, we recite the Beracha of "Shehehiyanu." Seemingly, this should apply to Sefirat Ha’omer, as well, yet Halacha does not require reciting this Beracha before the counting of the Omer. The reason is that when we count the Omer, we are mindful of the fact that we count only as a commemoration of the actual Misva, which we cannot fulfill in its true form due to the absence of the Bet Hamikdash. The counting of the Omer thus evokes a degree of sorrow, and does not warrant the recitation of the festive "Shehehiyanu" blessing.
Summary: It is customary to recite immediately after Sefirat Ha’omer a brief prayer for the rebuilding of the Bet Hamikdash: "Harahaman Hu Yahazir Abodat Bet Hamikdash Limkomah Bimhera Beyamenu Amen."
